def run():
gd = GenericDialogPlus("ND2 Conversion Tool")
gd.addMessage("This plugin uses BioFormats to convert ND2 images to JPEG for further processing in ImageJ.")
gd.addDirectoryOrFileField("Input: ", "G:\\Subdir testing\\") #srcDir
gd.addDirectoryOrFileField("Output: ", "G:\\Subdir testing\\") #dstDir
gd.addStringField("File name contains: ", "") #nameContains
gd.addCheckbox("Preserve directory structure?", True) #keepDirs
gd.addCheckbox("Run in headless mode?", True) #anneBoleyn
gd.addCheckbox("Overwrite existing output files?", True)
gd.showDialog()
if gd.wasCanceled():
return
srcDir = gd.getNextString()
dstDir = gd.getNextString()
nameContains = gd.getNextString()
keepDirectories = gd.getNextBoolean()
anneBoleyn = gd.getNextBoolean()
overOut = gd.getNextBoolean()
IJ.run("Input/Output...", "jpeg=100")
for root, directories, filenames in os.walk(srcDir):
for filename in filenames:
# Check for file extension
if not filename.endswith(".nd2"):
continue
# Check for file name pattern
if nameContains not in filename:
continue
process(srcDir, dstDir, nameContains, root, filename, keepDirectories, anneBoleyn, overOut)
def get_user_params(event):
""" Allows user to select file and user parameters
Parameters
----------
event : Event
Waits for get_user_params_JB JButton to be pressed
Returns
-------
dict
Dict containing filename, number of Gaussians to fit,
% of dataset to import, whether to specify grey value
limits, minimum grey value and maximum grey value to
consider (optional)
"""
# Open user dialog
gui = GenericDialogPlus("Define user parameters")
gui.addFileField("Image filename", "Select image file")
gui.addNumericField("Number of Gaussians to fit: ", 2, 0)
gui.addNumericField("Percentage of dataset to import: ", 15, 0)
gui.addCheckbox("Specify grey value limits?", False)
gui.addNumericField("Min grey value (optional): ", 0, 0)
gui.addNumericField("Max grey value (optional): ", 255, 0)
gui.showDialog()
# Extract user parameters
if gui.wasOKed():
user_params = {} # empty dict
user_params['img_fname'] = str(gui.getNextString())
user_params['n_gaussians'] = int(gui.getNextNumber())
user_params['pct_stack_import'] = float(gui.getNextNumber())
user_params['specify_gv'] = gui.getNextBoolean()
user_params['min_gv'] = float(gui.getNextNumber())
user_params['max_gv'] = float(gui.getNextNumber())
# Create results directory
results_dir = os.path.splitext(user_params['img_fname'])[0] + "_results"
if os.path.isdir(results_dir) == False:
os.mkdir(results_dir)
print("Results directory: {}".format(results_dir))
# Write user parameters to text file
user_params_fname = os.path.join(results_dir, "Users_Params.csv")
with open(user_params_fname, "wb") as f:
w = csv.DictWriter(f, user_params.keys())
w.writeheader()
w.writerow(user_params)
# Write directory to look for user params to text file in main/
temp_user_dir = os.path.join(os.path.dirname(__file__),
"temp_user_dir.txt")
if os.path.isfile(temp_user_dir) == True:
os.remove(temp_user_dir) # delete temp_user_dir.txt if present
f = open(temp_user_dir, "w")
f.write(user_params_fname)
f.close()
return user_params
def make_dialog():
parameters = {}
gd = GenericDialogPlus("Grid Stitch SDC Data")
gd.addMessage( "Warning!\n"\
"In order to display a fused image upon completion of stitching\n"\
"please disable Fiji's ImageJ2 options. When enabled an ImageJ\n"\
"exception will be displayed upon completion. This exception can\n"
"be safely ignored.")
gd.addMessage( "Information\n"\
"This plugin is a wrapper around the Fiji 'Grid Stitching' plugin.\n"\
"It allows tiles generated in SlideBook to be directly stitched by\n"\
"by first writing out the individual tiles, executing the 'Grid Stitching'\n"\
"plugin and writing the fused image to disk.")
gd.addMessage("")
gd.addNumericField("grid_size_x", 3, 0)
gd.addNumericField("grid_size_y", 3, 0)
gd.addCheckbox("Select channel",False)
gd.addNumericField("", 0, 0)
gd.addCheckbox("Are the Z slices separate files?",False)
gd.addDirectoryField("directory", "", 50)
gd.showDialog()
if (gd.wasCanceled()): return
parameters['gridX'] = int(math.ceil(gd.getNextNumber()))
parameters['gridY'] = int(math.ceil(gd.getNextNumber()))
parameters['select_channel'] = gd.getNextBoolean()
parameters['channel'] = None
if parameters['select_channel']:
parameters['channel'] = int(gd.getNextNumber())
parameters['separate_z'] = gd.getNextBoolean()
directory = str(gd.getNextString())
if directory is None:
# User canceled the dialog
return None
else:
directory = os.path.abspath(directory)
parameters['directory'] = directory + os.path.sep
return parameters
def get_parameters(p):
gd = GenericDialogPlus("Please enter parameters")
for k in p['expose_to_gui']['value']:
if p[k]['type'] == 'boolean':
gd.addCheckbox(k, p[k]['value'])
elif p[k]['type'] == 'folder':
gd.addDirectoryField(k, p[k]['value'], 100)
elif p[k]['type'] == 'file':
gd.addFileField(k, p[k]['value'], 100)
elif p[k]['type'] == 'string':
if p[k]['choices']:
gd.addChoice(k, p[k]['choices'], p[k]['value'])
else:
gd.addStringField(k, p[k]['value'])
elif p[k]['type'] == 'int':
if p[k]['choices']:
gd.addChoice(k, p[k]['choices'], p[k]['value'])
else:
gd.addNumericField(k, p[k]['value'], 0)
elif p[k]['type'] == 'float':
gd.addNumericField(k, p[k]['value'], 2)
gd.showDialog()
if gd.wasCanceled():
return
for k in p['expose_to_gui']['value']:
if p[k]['type'] == 'boolean':
p[k]['value'] = gd.getNextBoolean()
elif p[k]['type'] == 'folder' or p[k]['type'] == 'file':
p[k]['value'] = gd.getNextString()
elif p[k]['type'] == 'string':
if p[k]['choices']:
p[k]['value'] = gd.getNextChoice()
else:
p[k]['value'] = gd.getNextString()
elif p[k]['type'] == 'int':
if p[k]['choices']:
p[k]['value'] = int(gd.getNextChoice())
else:
p[k]['value'] = int(gd.getNextNumber())
elif p[k]['type'] == 'float':
p[k]['value'] = gd.getNextNumber()
return p
Win.addCheckbox("Add_ROI detected to ROI manager",
prefs.getInt("AddRoi", True))
Win.addCheckbox("Show_result table", prefs.getInt("ShowTable", False))
Win.addMessage("""If you use this plugin please cite :
Laurent SV Thomas, Jochen Gehrig
bioRxiv 619338; doi: https://doi.org/10.1101/619338""")
Win.addHelp(
"https://github.com/multi-template-matching/MultiTemplateMatching-Fiji/wiki"
)
Win.showDialog()
if Win.wasOKed():
template = Win.getNextImage()
image = Win.getNextImage()
flipv = Win.getNextBoolean()
fliph = Win.getNextBoolean()
angles = Win.getNextString()
method = Win.getNextChoice()
n_hit = int(Win.getNextNumber())
score_threshold = Win.getNextNumber()
#tolerance = Win.getNextNumber()
tolerance = 0
max_overlap = Win.getNextNumber()
add_roi = Win.getNextBoolean()
show_table = Win.getNextBoolean()
# Save for persistence
ImageName = image.getTitle()
prefs.put("Template", template.getTitle())
prefs.put("Image", ImageName)
gd.addMessage("Start by choosing a registration directory or images directory!")
statusf=gd.getMessage()
gd.showDialog()
if gd.wasCanceled():
sys.exit("User cancelled!")
# Process Dialog Choices
rootDir=gd.getNextString()
os.chdir(rootDir)
refBrain=gd.getNextString()
image=gd.getNextString()
image=relpath(image,rootDir)
print refBrain
refBrain=relpath(refBrain,rootDir)
print refBrain
affine=gd.getNextBoolean()
ch01=gd.getNextBoolean()
warp=gd.getNextBoolean()
ch02=gd.getNextBoolean()
reformat=gd.getNextBoolean()
ch03=gd.getNextBoolean()
munger_actions=""
if affine:
munger_actions+="-a "
if warp:
munger_actions+="-w "
if reformat:
channels=''
if ch01:
channels+='01'
if ch02:
gdp.addStringField("Channel 2:", 'B', 8)
gdp.addStringField("Channel Z/Channel W:", 'C', 8)
gdp.addToSameRow()
gdp.addStringField("R/R0:", 'D', 8)
gdp.showDialog()
if gdp.wasOKed():
dest = gdp.getNextString().strip()
ProFolder = gdp.getNextString().strip()
Procsv = gdp.getNextString().strip()
radius = int(gdp.getNextString().strip())
interval = int(gdp.getNextString().strip())
errorval = gdp.getNextString().strip()
f_f = gdp.getNextRadioButton()
back_state = gdp.getNextString().strip()
back_val = int(gdp.getNextString().strip())
blur_state = gdp.getNextBoolean()
blur_val = int(gdp.getNextString().strip())
r_start = int(gdp.getNextString().strip())
r_end = int(gdp.getNextString().strip())
ch1_str = gdp.getNextString().strip()
ch2_str = gdp.getNextString().strip()
ch12_str = gdp.getNextString().strip()
rr0_str = gdp.getNextString().strip()
imp_save = IJ.getImage()
Save_Title = imp_save.getTitle()
try:
erroval = int(errorval)
except ValueError:
errorval = errorval
gd.addChoice("Nuclear thresholding method", methodsList, nucMethod)
gd.addCheckbox("Threshold nuclei by stack?", analyzeNucStack)
gd.addCheckbox("Are the cardiomyocyte images brightfield?", brightfield)
gd.addChoice("Cardiomyocyte thresholding method", methodsList, cmMethod)
gd.addCheckbox("Threshold cardiomyocyes by stack?", analyzeCmStack)
gd.addNumericField("Rows per well", rowNo, 0)
gd.addNumericField("Columns per well", colNo, 0)
gd.addNumericField("Nuclear minimum size (pixels)", nucMinSize, 0)
gd.addNumericField("Cardiomyocyte minimum size (pixels)", cmMinSize, 0)
gd.showDialog()
folderPath = gd.getNextString() + "/"
formatString = gd.getNextString()
groupBy = re.findall(r"\w+", gd.getNextString())
nucChannel = gd.getNextString()
cmChannel = gd.getNextString()
stitched = gd.getNextBoolean()
nucMethod = gd.getNextChoice()
analyzeNucStack = gd.getNextBoolean()
brightfield = gd.getNextBoolean()
cmMethod = gd.getNextChoice()
analyzeCmStack = gd.getNextBoolean()
rowNo = int(gd.getNextNumber())
colNo = int(gd.getNextNumber())
nucMinSize = int(gd.getNextNumber())
cmMinSize = int(gd.getNextNumber())
allFileNames = os.listdir(folderPath)
jsonStoreDict = {"folderPath": folderPath,
"formatString":formatString,
"groupBy": ','.join(groupBy),
"nucChannel": nucChannel,
"cmChannel": cmChannel,
Win.addMessage("Outputs")
Win.addCheckbox("Open_images as a stack (must have identical sizes)", prefs.getInt("ShowImages", True))
Win.addCheckbox("Add_ROI detected to ROI Manager", prefs.getInt("AddRoi", True))
Win.addCheckbox("Show_result table", prefs.getInt("ShowTable", False))
Win.addMessage("""If you use this plugin please cite :
Laurent SV Thomas, Jochen Gehrig
bioRxiv 619338; doi: https://doi.org/10.1101/619338""")
Win.addHelp("https://github.com/multi-template-matching/MultiTemplateMatching-Fiji/wiki")
Win.showDialog()
if Win.wasOKed():
TemplatePath = Win.getNextString()
ImagePath = Win.getNextString()
RoiPath = Win.getNextString()
flipv = Win.getNextBoolean()
fliph = Win.getNextBoolean()
angles = Win.getNextString()
method = Win.getNextChoice()
n_hit = int(Win.getNextNumber())
score_threshold = Win.getNextNumber()
#tolerance = Win.getNextNumber()
tolerance = 0
max_overlap = Win.getNextNumber()
show_images = Win.getNextBoolean()
add_roi = Win.getNextBoolean()
show_table = Win.getNextBoolean()
# Save for persistence
prefs.put("TemplatePath", TemplatePath)
prefs.put("ImagePath", ImagePath)
import os, shutil
import uuid
import sys
gdp=GenericDialogPlus("File Randomizer")
file_type = gdp.getNextString()
gdp.addStringField("File Extension ", '.tif',5)
x=gdp.addDirectoryField("Source:", " ")
gdp.addDirectoryField("Destination:", "(optional)")
gdp.addCheckbox("Copy & Move",False)
gdp.showDialog()
if gdp.wasOKed():
file_type = gdp.getNextString().strip()
source_path = gdp.getNextString().strip()
dest_path = gdp.getNextString().strip()
copymove=gdp.getNextBoolean()
if dest_path == '(optional)':
dest_path = source_path
else:
exit()
##makes a new directory in the destination directory, called randomized.
key='key.csv'
r_key= os.path.join(dest_path,key)
if copymove ==True:
randomized = 'randomized'
path = os.path.join(dest_path,randomized)
path = path+'/'
try:
'(' + str(progress[2]) + '/' + str(progress[1]) + ')', italicFont)
gdp.addHelp("https://github.com/JohnSargeant-rgb")
gdp.showDialog()
if gdp.wasOKed():
dest = gdp.getNextString().strip()
ProFolder = gdp.getNextString().strip()
Quant = gdp.getNextString().strip()
Quant_MM = gdp.getNextString().strip()
transport_c = gdp.getNextChoice()
file_type = gdp.getNextString().strip()
golgi_c = gdp.getNextChoice()
extension = gdp.getNextString().strip()
zoom_to = int(gdp.getNextChoice())
radius = gdp.getNextString().strip()
color_scale = gdp.getNextChoice()
always_select = gdp.getNextBoolean()
always_auto = gdp.getNextBoolean()
mean_max_det = gdp.getNextBoolean()
man_bck_det = gdp.getNextBoolean()
auto_pos_det = gdp.getNextBoolean()
xpos_det = gdp.getNextString().strip()
ypos_det = gdp.getNextString().strip()
new_selected_values = {
"ProFolder_def": ProFolder,
"Quant_def": Quant,
"Quant_MM_def": Quant_MM,
"tran_def": transport_c,
"file_def": file_type,
"golgi_def": golgi_c,
"ext_def": extension,
gdp=GenericDialogPlus("File Derandomizer")
gdp.addFileField("'Key' path :", " ")
gdp.addFileField("Data file :", " ")
gdp.addDirectoryField("Derandomized path", "(optional)")
gdp.addDirectoryField("Processed Image Folder", " ")
gdp.addCheckbox("Derandomize Data File", True)
gdp.addCheckbox("Derandomize Image Folder", False)
gdp.showDialog()
if gdp.wasOKed():
key_path = gdp.getNextString().strip()
data_path = gdp.getNextString().strip()
deR_path = gdp.getNextString().strip()
pi_path= gdp.getNextString().strip()
ddf=gdp.getNextBoolean()
dif=gdp.getNextBoolean()
if deR_path == "(optional)":
deR_path = os.path.dirname(data_path)
else:
exit()
# function to return key for any value
def get_key(val):
for key, value in random.items():
if val == value:
return key
def replace(text,dic):
"""Replaces values with keys"""
"Start by choosing a registration directory or images directory!")
statusf = gd.getMessage()
gd.showDialog()
if gd.wasCanceled():
sys.exit("User cancelled!")
# Process Dialog Choices
rootDir = gd.getNextString()
os.chdir(rootDir)
refBrain = gd.getNextString()
image = gd.getNextString()
image = relpath(image, rootDir)
print refBrain
refBrain = relpath(refBrain, rootDir)
print refBrain
affine = gd.getNextBoolean()
ch01 = gd.getNextBoolean()
warp = gd.getNextBoolean()
ch02 = gd.getNextBoolean()
reformat = gd.getNextBoolean()
ch03 = gd.getNextBoolean()
munger_actions = ""
if affine:
munger_actions += "-a "
if warp:
munger_actions += "-w "
if reformat:
channels = ''
if ch01:
channels += '01'
if ch02:
